GapMind for catabolism of small carbon sources

 

Alignments for a candidate for actP in Echinicola vietnamensis KMM 6221, DSM 17526

Align Acetate uptake permease, ActP1; also takes up tellurite (characterized)
to candidate Echvi_1267 Echvi_1267 probable sodium:solute symporter, VC_2705 subfamily

Query= TCDB::D5AU53
         (551 letters)



>FitnessBrowser__Cola:Echvi_1267
          Length = 567

 Score =  189 bits (480), Expect = 2e-52
 Identities = 149/523 (28%), Positives = 237/523 (45%), Gaps = 88/523 (16%)

Query: 35  WTAIAMFLFFVVATLILTGWAARRTKSTADFYTAGGGITGFQNGLAIAGDYMSAAAFLGI 94
           WT I + L F +   I   W+  R  ST +FY AGGG++   NG+A   D+MSAA+F+ +
Sbjct: 6   WTYILVGLSFALYIGIAI-WS--RAGSTKEFYVAGGGVSPLANGMATGADWMSAASFISM 62

Query: 95  SGMVFAKGVDGAIYTVGFTVGWPFILFLIAERLRNLGKFTFADITSFRLEQTRIRTLSAL 154
           +G++   G DG++Y +G+T G+  +  L+A  LR  GKFT  D    R    + R ++  
Sbjct: 63  AGLISFMGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFVGDRYYSNKARVVAVF 122

Query: 155 GALTVVVFYLIAQMVGAGKLIQLLFGLPYSYAVILVGVLMVLYVTFGGMLATTWVQIVKA 214
            A+ +   Y+  QM G G +      +  +  VI+   ++  Y   GGM   T+ Q+ + 
Sbjct: 123 CAIFISFTYVAGQMRGVGIVFSRYLEVDINTGVIIGMCIVFFYAVLGGMKGITYTQVAQY 182

Query: 215 VMLLSGATLLVILGLAQFGFSPERLMADALANHAKGAAILEPTPLVTDWVSGV------- 267
            +L+    +  I       F   +L ++ +     G  + + T L+ D + GV       
Sbjct: 183 CVLIFAFMVPAI-------FISMQLTSNPIPQLGLGGTVADGTYLL-DKLDGVLTDLGFH 234

Query: 268 -------------SLALALMFGPAGLPHILMRFFTVPDAKEARKSVFYATGFVAYFFVLT 314
                        ++ LALM G AGLPH+++RFFTVP  K+AR S  YA  F+A  +   
Sbjct: 235 AYTSGKKSMGDMFAITLALMVGTAGLPHVIVRFFTVPRVKDARLSAGYALVFIAILYTTA 294

Query: 315 TTIG----FLAITLVGKNP-------------------------------------EFLD 333
             +     + AI  V + P                                     EF  
Sbjct: 295 PAVSAFGIYNAIDSVSEKPIDDLPEWVTNWQQTQLIKINDKNQDGVVQYVADPERNEFTI 354

Query: 334 AKGIIGGGNMAAIHLAQAVGGNIFLGFISAVAFATILAVVSGLALSGASAVAHDLYANVV 393
            K I+   N     L      N  +G ++A   A  L+  +GL L  +++V+ DL  N  
Sbjct: 355 DKDIMVLANPEIAQLP-----NWVVGLVAAGGMAAALSTAAGLLLVISTSVSRDLAKNF- 408

Query: 394 KKGAAADKAEMRVSRIATLVLGVLAIVLGLMFENQNIAFMVGLAFGLAASVNFPVLLLSI 453
                +DK E+ ++R+A  V  ++A   G+      +A +V  AFGLAA+  FPV+++ I
Sbjct: 409 -NPGISDKKELLIARVAAAVAVIVAGYFGVN-PPGFVAEVVAFAFGLAAASFFPVIIMGI 466

Query: 454 FWKGMTTRGAFIGGLIGLVVSIVLVVLGPAVWVDVFKFDTPIF 496
           F K M   GA  G L+GLV ++  ++         FKF T +F
Sbjct: 467 FSKRMNKEGAIWGMLVGLVFTLSYII--------YFKFGTDLF 501


Lambda     K      H
   0.328    0.140    0.414 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 814
Number of extensions: 41
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 567
Length adjustment: 36
Effective length of query: 515
Effective length of database: 531
Effective search space:   273465
Effective search space used:   273465
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory